Isolation of specific target particle populations, e.g., living cells or microvesicles, from complex mixtures such as whole blood has significant utility in both clinical practice and basic medical research. A variety of approaches may be used to separate particles from a heterogeneous sample. For example, some techniques can use functionalized materials to capture cells based on cell surface markers that are particular to the target cell population using specific capture moieties present on or in the functionalized materials. Such capture moieties can include antibodies or other specific binding molecules, such as aptamers or selectins. For example, a microfluidic affinity-based chip that is configured to isolate rare circulating tumor cells (CTCs) from whole blood of cancer patients is described, e.g., in Nagrath et al., “Isolation of rare circulating tumour cells in cancer patients by microchip technology,” Nature 450 (2007), pp. 1235-1239, or Stott et. al., “Isolation of circulating tumor cells using microvortex-generating herringbone-chip,” PNAS 107 (2010), pp. 18392-18397. These CTCs may disseminate from the tumor and are observed to be present in numbers that tend to correlate with patients' clinical courses. These CTCs may also be involved in metastasis. Accordingly, such microfluidic chip technology may be used in diagnostic and prognostic devices for oncological applications. At present, limited phenotyping and genotyping of these rare cells can be achieved because the CTCs tend to remain attached to the substrate (e.g., a silicon-based chip).